Discussion:
[gmx-users] Frozen groups lead to a high energy
Sam David
2018-11-29 23:23:51 UTC
Permalink
Dear gromacs users
I'm simulation a hydrocarbon and water mixture placed on a slab of metal.
The metal surface is frozen in the z-direction. Energy minimization works
with no errors but I see the potential energy is too high as below.

Steepest Descents converged to machine precision in 1754 steps,
but did not reach the requested Fmax < 1.
Potential Energy = 1.9604517e+08
Maximum force = 3.1745122e+03 on atom 23433
Norm of force = 3.8078518e+01

After energy minimization, I did short nvt followed by short npt then npt
production. I tried several times and different parameters to reduce the
energy of the system but still very high as below:

Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. Improper Dih.
2.07807e+08 2.96662e+05 8.57456e+02 2.50326e+04 1.60567e+02
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
4.33776e+04 -7.73429e+03 3.05165e+11 -1.07225e+04 -1.24055e+07
Coul. recip. Potential Kinetic En. Total Energy Temperature
5.93613e+03 3.05360e+11 1.97149e+05 3.05361e+11 3.88708e+02
Pres. DC (bar) Pressure (bar) Constr. rmsd
-2.71515e+02 3.08812e+10 4.72857e-06

However, when I remove frozen groups, potential energy becomes negative

Any ideas on how to reduce system energy while using freeze groups option!


Thank you
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Justin Lemkul
2018-11-30 19:28:59 UTC
Permalink
Post by Sam David
Dear gromacs users
I'm simulation a hydrocarbon and water mixture placed on a slab of metal.
The metal surface is frozen in the z-direction. Energy minimization works
with no errors but I see the potential energy is too high as below.
Steepest Descents converged to machine precision in 1754 steps,
but did not reach the requested Fmax < 1.
Potential Energy = 1.9604517e+08
Maximum force = 3.1745122e+03 on atom 23433
Norm of force = 3.8078518e+01
After energy minimization, I did short nvt followed by short npt then npt
production. I tried several times and different parameters to reduce the
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. Improper Dih.
2.07807e+08 2.96662e+05 8.57456e+02 2.50326e+04 1.60567e+02
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
4.33776e+04 -7.73429e+03 3.05165e+11 -1.07225e+04 -1.24055e+07
Coul. recip. Potential Kinetic En. Total Energy Temperature
5.93613e+03 3.05360e+11 1.97149e+05 3.05361e+11 3.88708e+02
Pres. DC (bar) Pressure (bar) Constr. rmsd
-2.71515e+02 3.08812e+10 4.72857e-06
However, when I remove frozen groups, potential energy becomes negative
Any ideas on how to reduce system energy while using freeze groups option!
Freezing is an artificial perturbation that, in your case, may be
preventing an unfavorable clash from being resolved.

-Justin
--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

***@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================
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Sam David
2018-11-30 20:47:39 UTC
Permalink
Dear Justin,
Thank you for your answer.

I will try position restraints which could be better for my case but I'm
not sure how to get force constants.
Any ideas

Best
Post by Sam David
Post by Sam David
Dear gromacs users
I'm simulation a hydrocarbon and water mixture placed on a slab of metal.
The metal surface is frozen in the z-direction. Energy minimization works
with no errors but I see the potential energy is too high as below.
Steepest Descents converged to machine precision in 1754 steps,
but did not reach the requested Fmax < 1.
Potential Energy = 1.9604517e+08
Maximum force = 3.1745122e+03 on atom 23433
Norm of force = 3.8078518e+01
After energy minimization, I did short nvt followed by short npt then npt
production. I tried several times and different parameters to reduce the
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. Improper
Dih.
Post by Sam David
2.07807e+08 2.96662e+05 8.57456e+02 2.50326e+04
1.60567e+02
Post by Sam David
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb
(SR)
Post by Sam David
4.33776e+04 -7.73429e+03 3.05165e+11 -1.07225e+04
-1.24055e+07
Post by Sam David
Coul. recip. Potential Kinetic En. Total Energy
Temperature
Post by Sam David
5.93613e+03 3.05360e+11 1.97149e+05 3.05361e+11
3.88708e+02
Post by Sam David
Pres. DC (bar) Pressure (bar) Constr. rmsd
-2.71515e+02 3.08812e+10 4.72857e-06
However, when I remove frozen groups, potential energy becomes negative
Any ideas on how to reduce system energy while using freeze groups
option!
Freezing is an artificial perturbation that, in your case, may be
preventing an unfavorable clash from being resolved.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
==================================================
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* Please search the archive at
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posting!
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